int VennCommand::execute(){
try {
- int count = 1;
+ int count = 1;
+ SAbundVector* lastSAbund;
+ vector<SharedRAbundVector*> lastLookup;
//if the users entered no valid calculators don't execute command
if (vennCalculators.size() == 0) { return 0; }
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
+ lastLookup = lookup;
}else if (format == "list") {
//you are using just a list file and have only one group
read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
sabund = globaldata->sabund;
+ lastSAbund = globaldata->sabund;
input = globaldata->ginput;
}
-
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = globaldata->labels;
if (format != "list") {
- while(lookup[0] != NULL){
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
-
cout << lookup[0]->getLabel() << '\t' << count << endl;
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
if (lookup.size() > 4) {
cout << "Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile." << endl;
- for (int i = lookup.size(); i > 3; i--) { delete lookup[i]; lookup.pop_back(); }
+ for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
}
-
- //util->getSharedVectors(globaldata->Groups, lookup, order); //fills group vectors from order vector.
venn->getPic(lookup, vennCalculators);
}
- //prevent memory leak
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
+ cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+ processedLabels.insert(lastLookup[0]->getLabel());
+ userLabels.erase(lastLookup[0]->getLabel());
+
+ if (lastLookup.size() > 4) {
+ cout << "Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile." << endl;
+ for (int i = lastLookup.size(); i > 4; i--) { lastLookup.pop_back(); } //no memmory leak because pop_back calls destructor
+ }
+ venn->getPic(lastLookup, vennCalculators);
+ }
+ //prevent memory leak
+ if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
+ lastLookup = lookup;
+
//get next line to process
lookup = input->getSharedRAbundVectors();
count++;
}
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ cout << "Your file does not include the label "<< *it;
+ if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
+ cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ needToRun = true;
+ }else {
+ cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+ if (lastLookup.size() > 4) {
+ cout << "Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile." << endl;
+ for (int i = lastLookup.size(); i > 3; i--) { delete lastLookup[i]; lastLookup.pop_back(); }
+ }
+ venn->getPic(lastLookup, vennCalculators);
+ }
+
+ for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
+
//reset groups parameter
globaldata->Groups.clear();
}else{
- while(sabund != NULL){
+ while((sabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){
cout << sabund->getLabel() << '\t' << count << endl;
venn->getPic(sabund, vennCalculators);
+
+ processedLabels.insert(sabund->getLabel());
+ userLabels.erase(sabund->getLabel());
}
- delete sabund;
+ if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastSAbund->getLabel()) != 1)) {
+
+ cout << lastSAbund->getLabel() << '\t' << count << endl;
+ venn->getPic(lastSAbund, vennCalculators);
+
+ processedLabels.insert(lastSAbund->getLabel());
+ userLabels.erase(lastSAbund->getLabel());
+ }
+
+ if (count != 1) { delete lastSAbund; }
+ lastSAbund = sabund;
+
sabund = input->getSAbundVector();
count++;
}
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ cout << "Your file does not include the label "<< *it;
+ if (processedLabels.count(lastSAbund->getLabel()) != 1) {
+ cout << ". I will use " << lastSAbund->getLabel() << "." << endl;
+ needToRun = true;
+ }else {
+ cout << ". Please refer to " << lastSAbund->getLabel() << "." << endl;
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ cout << lastSAbund->getLabel() << '\t' << count << endl;
+ venn->getPic(lastSAbund, vennCalculators);
+ }
+ delete lastSAbund;
}
+
globaldata->setGroups("");
return 0;
}
projects / mothur.git / blobdiff